AW: [gmx-users] topology for a membrane + protein

[Justin A. Lemkul]

The Gromos parameters do not replicate lipid properties well, so I would 
recommend not using PRODRG for the lipids, unless your intent is to refine those 
parameters to make them work :)

There are numerous reports in the literature of treating the protein with 
Gromos96 (your choice of parameter set, I have seen almost all of them).  You 
can also follow Chris Neale's protocol for converting the lipid.itp parameters 
to the format required (and compatible with) OPLS.  Search the list archive and 
you will find it.  Other useful information is here:

http://wiki.gromacs.org/index.php/Membrane_Simulations

-Justin

serdar durdagi wrote:
> you may try prodrg beta to get Gromos96 ff for your lipid.
> 
>  
> 
> serdar
> 
> 
> --- Rebeca García Fandiño /<regafan at hotmail.com>/ schrieb am *Fr, 11.7.2008:
> *
> 
>     *Von: Rebeca García Fandiño <regafan at hotmail.com>
>     Betreff: [gmx-users] topology for a membrane + protein
>     An: gmx-users at gromacs.org
>     Datum: Freitag, 11. Juli 2008, 11:14
> 
>     *
>     *
> 
> 
>     *
> 
>     *Hello,*
> 
>     *I am a new user of Gromacs, and I am trying to simulate a system of
>     a membrane composed by POPC, cholesterol and sphingomyelin and a
>     protein. I am using lipid.itp, but it includes ffgmx.itp, and I have
>     read it is deprecated, so I am having a lot of problems to introduce
>     the protein topology with ffG43a1 or opls, without using ffgmx.itp
>     also for the protein. *
> 
>     *I would like to know which is the recommendation, because I am a
>     bit confused about this, an in the case of using a different force
>     field from the deprecated ffgmx for the protein, does anybody know
>     where I could get the paremeters for the Berger lipids constructed
>     with a more modern forcefield than ffgmx?*
> 
>     *I hope somebody could help me, I will really appreciate your advices.*
> 
>     *Best wishes, *
> 
>     * *
> 
>     *Rebeca Garcia*
> 
>     *Parc Cientific de Barcelona *
> 
>     *Universidad de Barcelona*
> 
>     *regafan at hotmail.com*
> 
>     *
>     *
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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